[HN Gopher] Researchers use genomes of 241 species to redefine m...
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Researchers use genomes of 241 species to redefine mammalian tree
of life
Author : wglb
Score : 102 points
Date : 2023-05-13 01:18 UTC (1 days ago)
(HTM) web link (phys.org)
(TXT) w3m dump (phys.org)
| vrglvrglvrgl wrote:
| [dead]
| thriftwy wrote:
| Euarchontoglira would be a way less researched and relevant
| branch of life have it not produced us humans.
|
| Same thing that if sentient birds were to appear, they will
| consider dinosaur epoch never ended, just had a setback and
| useful bottleneck.
| jjtheblunt wrote:
| Are African Greys sentient bird examples?
| thriftwy wrote:
| Did they manage to build and publish an evolution tree?
| jjtheblunt wrote:
| I think that's beyond the meaning of sentient.
| Xorakios wrote:
| "sentient" is often used casually when "sapient" is meant
|
| don't whether that's country-level language variation, an
| example of language evolution ;), or just sloppiness.
| thriftwy wrote:
| "Sapient" is a stupid term because a Denisovian or
| Neanderthal were likely able to produce a piece of
| research with some assistance, while being a Homo {not
| Sapient}.
| sandworm101 wrote:
| >> way less researched and relevant branch of life have it not
| produced us humans.
|
| I doubt that _any_ branch would have been even studied in any
| way had not euarchontoglira produced us humans. I doubt many
| other animals are even aware of evolution as a concept.
| AtlasBarfed wrote:
| >> sentient birds
|
| have you seen the problem solving of crows?
|
| edit: vid: https://www.youtube.com/watch?v=Gui3IswQ0DI
| thriftwy wrote:
| Where can I read any science written by crows?
| bckr wrote:
| I think you're not using "sentience" in the same way as
| each other.
|
| I recommend avoiding "sentience" in this thread and being
| more specific about what you mean.
| fastaguy88 wrote:
| Building evolutionary trees from genomes is challenging, in part
| because of the difficulties inferring trees when different parts
| of the genome may be evolving at very different rates, but also
| because of the wide dynamic range of genome quality. Human and
| mouse genomes have far fewer errors (missing regions) than rat
| and cow, and many of the other several hundred genomes will be of
| much much lower quality. At this scale, it is difficult to know
| whether surprising results reflect biology or inaccuracy.
| inciampati wrote:
| A flip side of constraint is constrained diversity. Does a tree
| always work? Where are the genomes in ILS? Those will be very
| interesting regions.
| inciampati wrote:
| From the abstract: "However, because these approaches infer a
| single best tree, they mask signatures of phylogenetic conflict
| that result from incomplete lineage sorting and historical
| hybridization."
|
| So it can't be avoided, and the solution of making more trees
| from different stuff is somewhat unsatisfying. They have to
| work with the methods they have today.
| f6v wrote:
| They used maximum likelihood tree building. In Bayesian
| approach it's possible to sample from a distribution of trees
| which can help with the uncertainty. Anyway, I only have very
| limited knowledge on this from my evolutionary biology
| course.
| runeblaze wrote:
| Reading the paper I think they used both SVDquartets
| (coalescence-based explicitly for ILS) and concatenation +
| maximum likelihood, which is a very sane combination for
| the analysis. Not contradicting you here, but at their
| scale it is unlikely any Bayesian approach will converge,
| so they had to settle with whatever they had to quantify
| uncertainty (branch supports and others).
|
| Edit: and also the Bayesian approaches might have model
| mismatch, for example I am not sure what's an accurate
| Bayesian method that models hybridization and ILS
| sandworm101 wrote:
| Trees are tricky. They assume solid splits between species.
| While that may work well across millions/billions of years it
| does not work well when describing the specifics of split
| points. There is no bright line when one generation is suddenly
| a different species than the last. Genetics describes the slow
| accumulation of changes. Translating that into a tree of lines
| connected by points will always require compromise.
| mkl wrote:
| So horses are closer to lions than to antelopes? The pictures on
| phys.org and in the Science article preview are frustratingly
| unclear; most leaves of the tree are unlabelled.
| cjbgkagh wrote:
| I think the layout is optimized for showing branches event and
| not relative difference between species, though as a side
| effect of showing branching it does somewhat approximate
| relative difference.
| akiselev wrote:
| Sort of - it's more accurate to say that the order
| _Perissodactyla_ (containing horses) shares a common ancestor
| with the order _carnivora_ labeled #4 in the picture. Both of
| them share a common ancestor with _artiodactyla_ (even toed
| ungulates like antelope) labeled #3.
|
| They all differentiated over 60 million years ago, though,
| which was enough time for mammals to split into herbivores and
| carnivores and evolve back into sea animals like whales and
| dolphins. With converging and diverging evolution over that
| kind of time span, saying an animal is "closer to" another over
| simplifies a lot of detail. One species' genetics might
| resemble one order while the slowly evolving genes used to
| identify evolutionary relationships place it in a second order.
| Myrmornis wrote:
| https://www.science.org/doi/10.1126/science.abl8189
|
| It looks like they looked at a larger amount of the genome, and
| still found that relationships at the level of Order and below
| were hard to be sure about, since different genomic regions
| disagreed. They then speculate that this is related to different
| geological / tectonic / geomorphological processes occurring at
| that point in history, compared to the time of the earlier
| divergences. It's a frustrating area of science; we've learned
| that the reality is that some aspects of evolutionary history are
| very hard to be sure about, but scientific publishing and careers
| require more interesting claims.
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